「fast」の検索結果

Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.

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SQLAlchemy 2.x patterns for async FastAPI projects: models, sessions, queries, bulk operations, transactions, and Alembic migrations. Trigger: When writing models, queries, bulk operations, or DB-touching service code.

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Enforces Pydantic v2 strict models, asynchronous dependency generators, and uv environment setup.

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Diagnoses and fixes UI performance across loading speed, rendering, animations, images, and bundle size. Use when the user mentions slow, laggy, janky, performance, bundle size, load time, or wants a faster, smoother experience.

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Two-dimensional minimalist style with vibrant colors, clean typography, and no 3D effects for fast, user-friendly interfaces.

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Fast headless browser for QA testing and site dogfooding. Navigate any URL, interact with elements, verify page state, diff before/after actions, take annotated screenshots, check responsive layouts, test forms and uploads, handle dialogs, and assert element states. ~100ms per command. Use when you need to test a feature, verify a deployment, dogfood a user flow, or file a bug with evidence. Use when asked to "open in browser", "test the site", "take a screenshot", or "dogfood this". (gstack)

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Fast headless browser for QA testing and site dogfooding. Navigate pages, interact with elements, verify state, diff before/after, take annotated screenshots, test responsive layouts, forms, uploads, dialogs, and capture bug evidence. Use when asked to open or test a site, verify a deployment, dogfood a user flow, or file a bug with screenshots. (gstack)

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Bulk-retouch a folder of portrait photos using Adobe tools — designed for wedding photographers and event photographers who need fast, walk-away batch processing. Use this skill when the user says "retouch my photos", "batch process these portraits", "process my wedding photos", "clean up this folder of images", "run my headshots through Adobe", or uploads/selects a folder of photos and wants them polished and ready to review. Automatically applies auto-straighten, auto-tone, and auto-light to every image. Outputs a preview grid and download folder. Access: 🔐 Signed-In required | Gen AI: ❌

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Designs or reviews CLIs so coding agents can run them reliably: non-interactive flags, layered --help with examples, stdin/pipelines, fast actionable errors, idempotency, dry-run, and predictable structure. Use when building a CLI, adding commands, writing --help, or when the user mentions agents, terminals, or automation-friendly CLIs.

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Run a fast, read-only health check across all skills in the library and produce a structured quality report — without modifying anything. Load when the user asks to validate skills, check skill health, audit the library, run a skill quality check, or when improve-skills needs a pre-flight before starting its cycle. Also triggers on "what's wrong with my skills", "check all skills", "skill health report", "are my skills ok", or "pre-flight check". Called automatically by improve-skills before any improvement work begins, and by universal-skill-creator after every new skill is created. Never modifies any file — only reads and reports.

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Tactical fast path: turn a small problem, bug report, edit request, or narrow refactor into three deliverables — a brief change-spec (docs/specs/), a detailed implementation-ready plan (docs/plans/), and a TODO.md with agent-pickable tasks and milestones. Load when the user describes a tactical problem and wants quick planning artifacts, says "plan this change", "create a TODO", "write a plan for this", "problem to plan", "break this into tasks for agents", "I want to change X — plan it", or when process-decomposer routes here after determining the user needs lightweight planning deliverables. Also triggers on "create tasks from this problem", "make this actionable", or "turn this into a plan agents can execute". For feature-sized work that needs an executable spec + constitution + cross-check gate, route to `spec-driven-development` (or `feature-spec`) instead.

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Design and implement CI/CD pipelines and automation — fast checks on every PR, safe releases, and repeatable workflows. Load when setting up GitHub Actions (or similar), adding pre-merge gates, automating releases, or the user asks "add CI", "set up workflows", "automate checks", "CD pipeline". Not for one-off local scripts (use task-specific tooling).

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Fast, modern JavaScript/TypeScript development with the Bun runtime, inspired by [oven-sh/bun](https://github.com/oven-sh/bun).

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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